Contacts of the helix formed by residues 192 - 209 (chain B) in PDB entry 2VZ6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B HIS* 3.3 73.0 + - + +
128B GLN* 5.4 0.2 - - - +
130B GLY* 5.0 0.8 - - - -
132B VAL* 3.7 22.4 - - + +
163B VAL* 4.1 12.6 - - + -
165B GLY* 3.6 17.6 + - - +
166B GLU* 3.1 39.6 + - - +
168B GLN* 4.6 2.2 - - - +
191B GLY* 1.3 71.0 - - - -
193B PRO* 1.4 71.5 - - + +
194B VAL* 3.0 1.8 + - - -
195B ASP* 3.2 11.3 + - - +
196B LEU* 4.0 1.4 + - + +
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Residues in contact with PRO 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN* 4.3 12.6 - - - +
183B GLU* 4.1 0.9 - - - +
191B GLY* 3.3 7.0 - - - +
192B LYS* 1.4 94.2 - - + +
194B VAL* 1.3 62.5 + - - +
196B LEU* 3.0 23.3 + - + +
197B TRP 3.2 3.8 + - - -
256B PRO* 3.8 34.3 - - + +
259B ARG* 2.8 34.5 + - + +
260B ILE 6.0 0.7 - - - +
261B THR* 6.5 1.1 - - + -
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 3.6 19.1 - - + -
134B ARG* 4.2 17.5 - - + +
179B TYR 4.9 1.6 - - - +
181B SER* 3.4 26.5 - - - +
183B GLU* 3.5 13.5 - - - +
184B VAL* 3.9 5.4 - - + -
190B TYR* 3.6 28.5 - - + -
191B GLY 3.3 18.2 - - - +
192B LYS 3.0 1.8 + - - -
193B PRO* 1.3 76.0 - - - +
195B ASP* 1.3 70.7 + - - +
197B TRP* 3.4 5.5 + - - +
198B ALA* 3.2 20.1 + - - +
259B ARG* 4.1 1.8 - - - +
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Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B VAL* 4.2 5.8 - - + +
126B CYS* 5.5 1.4 - - - +
127B HIS* 3.0 28.0 + - + +
131B VAL 4.6 0.2 - - - +
132B VAL* 3.5 9.2 - - - +
133B HIS* 2.9 29.8 + - - +
134B ARG* 2.9 30.1 + - - -
136B LEU* 3.6 20.8 + - + +
192B LYS 3.2 7.4 + - - +
193B PRO 3.1 0.2 - - - -
194B VAL* 1.3 79.3 - - - +
196B LEU* 1.3 57.2 + - - +
197B TRP 3.4 0.2 - - - -
198B ALA* 3.5 3.4 + - - -
199B CYS* 3.1 31.3 + - - -
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.8 26.5 - - + -
123B VAL* 4.7 2.7 - - + -
127B HIS* 3.8 25.1 - - + +
192B LYS* 4.4 3.1 - - + +
193B PRO* 3.0 13.2 + - + +
195B ASP* 1.3 74.6 - - - +
197B TRP* 1.3 66.1 + - - +
199B CYS* 3.4 3.4 + - + +
200B GLY 3.1 16.3 + - - -
251B MET* 3.6 19.0 - - + +
259B ARG* 4.0 10.1 - - + -
260B ILE* 3.6 35.4 - - + +
261B THR* 3.8 6.7 - - - +
262B ALA* 3.4 31.2 - - + +
265B ALA* 4.4 0.4 - - + -
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Residues in contact with TRP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLY 5.1 0.6 + - - -
179B TYR* 3.4 21.2 - - - +
180B LEU 3.2 17.1 + - - -
181B SER* 3.7 7.9 - - - -
182B PRO* 3.6 20.6 - - + -
193B PRO 3.2 5.7 + - - -
194B VAL 3.5 9.4 - - - +
195B ASP 3.4 0.2 - - - -
196B LEU* 1.3 77.0 - - - +
198B ALA* 1.3 61.9 + - - +
200B GLY 3.0 12.3 + - - -
201B VAL* 3.1 22.4 + - + +
213B PHE* 3.5 32.5 - + - -
225B ILE* 3.9 11.1 - - + +
228B GLY* 4.6 1.1 - - - -
251B MET 3.8 9.9 - - - -
252B LEU* 3.4 51.0 - - + +
253B THR 3.6 16.6 - - - -
254B ILE* 3.5 27.1 - - + -
259B ARG* 3.8 15.7 - - - +
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ARG 6.3 0.9 - - - -
136B LEU* 3.8 35.0 - - + +
179B TYR* 3.9 20.3 - - + +
194B VAL 3.2 9.9 + - - +
195B ASP* 3.8 9.9 - - - +
196B LEU 3.4 0.2 - - - -
197B TRP* 1.3 81.2 - - - +
199B CYS* 1.3 55.2 + - - +
201B VAL* 3.3 7.1 + - - +
202B ILE* 3.0 34.3 + - - +
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Residues in contact with CYS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 4.0 7.6 - - + +
119B ILE* 4.1 23.1 - - - -
120B LEU* 4.3 13.2 - - + -
123B VAL* 4.2 9.9 - - - -
136B LEU* 3.9 16.6 - - - -
195B ASP 3.1 25.9 + - - +
196B LEU* 3.7 8.3 - - - +
197B TRP 3.1 0.4 - - - -
198B ALA* 1.3 73.5 - - - +
200B GLY* 1.3 60.8 - - - +
202B ILE* 3.9 8.3 - - - +
203B LEU* 2.9 30.1 + - - +
251B MET* 3.9 19.3 - - + +
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Residues in contact with GLY 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU 3.1 6.3 + - - -
197B TRP 3.0 7.8 + - - -
199B CYS* 1.3 77.5 - - - +
201B VAL* 1.3 56.3 + - - +
203B LEU* 3.8 2.4 - - - +
204B TYR* 3.1 29.3 + - - +
248B ILE* 4.4 5.0 - - - +
251B MET* 3.6 28.0 - - - -
252B LEU* 3.9 14.9 - - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLY 3.8 18.8 - - - +
179B TYR* 3.6 29.4 - - + -
197B TRP* 3.1 36.7 + - + +
198B ALA* 3.3 7.8 + - - +
200B GLY* 1.3 75.3 - - - +
202B ILE* 1.3 60.5 + - - +
204B TYR* 3.4 4.0 + - - +
205B ILE* 3.1 30.5 + - + +
211B PRO* 5.1 2.5 - - + -
212B PRO* 3.6 30.5 - - + +
213B PHE* 4.3 3.6 - - + -
252B LEU* 4.0 7.0 - - + -
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 4.2 7.9 - - + -
116B ILE* 4.2 9.2 - - + -
119B ILE* 4.4 4.9 - - + -
136B LEU* 4.1 13.9 - - + -
137B LYS* 4.0 30.1 - - - +
138B PRO* 4.9 3.4 - - + -
141B LEU* 3.9 29.4 - - + -
179B TYR* 4.2 15.0 - - + -
198B ALA 3.0 22.0 + - - +
199B CYS* 3.9 9.9 - - - +
200B GLY 3.4 0.2 - - - -
201B VAL* 1.3 72.7 - - - +
203B LEU* 1.3 58.4 + - - +
205B ILE* 3.3 9.6 + - - +
206B LEU* 2.9 42.2 + - + +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 4.9 0.7 - - - +
116B ILE* 4.2 23.3 - - + -
199B CYS 2.9 18.8 + - - +
200B GLY 3.8 4.5 - - - +
202B ILE* 1.3 76.4 - - - +
204B TYR* 1.3 64.5 + - - +
206B LEU* 3.1 18.8 + - + +
207B LEU* 3.2 22.0 + - + +
244B ALA 4.7 2.0 - - - +
247B LEU* 4.1 32.8 - - + -
248B ILE* 3.8 23.8 - - + +
251B MET* 4.1 9.6 - - - -
270B TRP* 3.7 31.9 - - + -
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Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B GLY 3.1 18.7 + - - +
201B VAL 3.5 5.4 - - - +
203B LEU* 1.3 76.0 - - - +
205B ILE* 1.3 60.1 + - - +
207B LEU* 3.1 11.3 + - - +
208B VAL* 3.3 18.7 + - + +
210B TYR* 3.3 48.4 + + - -
212B PRO* 3.7 39.3 + - + +
230B TYR* 4.2 6.1 - + - -
231B ASP 2.7 28.9 + - - -
232B PHE* 3.9 7.4 - + - -
233B PRO* 4.4 1.0 - - - +
237B TRP* 3.5 25.5 + + - -
248B ILE* 3.9 28.0 - - + +
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PHE* 3.6 14.1 - - + -
138B PRO* 4.7 3.8 - - + -
179B TYR* 3.5 34.5 - - + +
201B VAL* 3.1 22.2 + - + +
202B ILE* 3.3 8.3 + - - +
204B TYR* 1.3 74.8 - - - +
206B LEU* 1.3 59.0 + - - +
209B GLY* 2.8 34.2 + - - -
210B TYR 3.6 7.6 - - - +
211B PRO* 3.7 25.6 - - + -
286B THR* 4.5 0.2 - - - +
290B LEU* 3.6 25.3 - - + +
293B PHE* 3.7 21.5 - - + -
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 4.6 4.0 - - + -
98B PHE* 3.8 23.8 - - + -
101B ILE* 3.4 32.8 - - + -
107B TYR* 2.7 39.3 + - - +
112B ALA* 4.3 13.2 - - + +
115B CYS* 4.1 22.9 - - + -
116B ILE* 4.2 15.3 - - + -
119B ILE* 4.8 2.9 - - + -
202B ILE* 2.9 29.5 + - + +
203B LEU* 3.1 11.4 + - + +
205B ILE* 1.3 76.9 - - - +
207B LEU* 1.3 61.8 + - - +
286B THR* 3.6 2.4 - - - +
290B LEU* 5.3 3.1 - - + -
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B TYR* 6.1 0.2 - - + -
109B GLU* 4.1 14.4 - - + -
112B ALA* 3.7 28.0 - - + -
203B LEU* 3.2 18.4 + - + +
204B TYR 3.1 7.7 + - - +
206B LEU* 1.3 79.2 - - - +
208B VAL* 1.3 56.7 + - + +
237B TRP* 4.2 10.8 - - + -
240B VAL* 4.1 15.5 - - + -
244B ALA* 3.6 29.4 - - + -
248B ILE* 4.0 19.3 - - + -
270B TRP* 4.1 13.0 - - + -
283B ARG* 3.0 21.1 + - - +
286B THR* 2.6 25.4 + - - +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B TYR* 3.3 23.1 + - + +
207B LEU* 1.3 84.9 - - + +
209B GLY* 1.3 59.7 + - - +
210B TYR* 3.6 38.7 + - + +
236B GLU* 4.1 15.8 - - + +
237B TRP* 3.3 45.3 - - + +
240B VAL* 4.5 0.7 - - + -
283B ARG* 4.1 12.3 - - - +
285B GLU 4.5 0.9 - - - +
286B THR* 3.6 13.9 + - - -
289B CYS* 3.7 10.4 - - - +
1302B PGO 5.1 3.1 + - - -
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Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ILE* 2.8 26.6 + - - -
208B VAL* 1.3 72.9 - - - +
210B TYR* 1.3 59.3 + - - +
286B THR* 3.8 14.6 - - - +
289B CYS* 3.5 23.4 - - - +
290B LEU* 3.6 16.4 - - - -
293B PHE* 3.6 14.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il